Meningococcus genome informatics platform: a system for analyzing multilocus sequence typing data

The Meningococcus Genome Informatics Platform (MGIP) is a suite of computational tools for the analysis of multilocus sequence typing (MLST) data, at http://mgip.biology.gatech.edu. MLST is used to generate allelic profiles to characterize strains of Neisseria meningitidis, a major cause of bacterial meningitis worldwide. Neisseria meningitidis strains are characterized with MLST as specific sequence types (ST) and clonal complexes (CC) based on the DNA sequences at defined loci. These data are vital to molecular epidemiology studies of N. meningitidis, including outbreak investigations and population biology. MGIP analyzes DNA sequence trace files, returns individual allele calls and characterizes the STs and CCs. MGIP represents a substantial advance over existing software in several respects: (i) ease of use—MGIP is user friendly, intuitive and thoroughly documented; (ii) flexibility—because MGIP is a website, it is compatible with any computer with an internet connection, can be used from any geographic location, and there is no installation; (iii) speed—MGIP takes just over one minute to process a set of 96 trace files; and (iv) expandability—MGIP has the potential to expand to more loci than those used in MLST and even to other bacterial species

sodC-Based Real-Time PCR for Detection of Neisseria meningitidis

Real-time PCR (rt-PCR) is a widely used molecular method for detection of Neisseria meningitidis (Nm). Several rt-PCR assays for Nm target the capsule transport gene, ctrA. However, over 16% of meningococcal carriage isolates lack ctrA, rendering this target gene ineffective at identification of this sub-population of meningococcal isolates. The Cu-Zn superoxide dismutase gene, sodC, is found in Nm but not in other Neisseria species. To better identify Nm, regardless of capsule genotype or expression status, a sodC-based TaqMan rt-PCR assay was developed and validated. Standard curves revealed an average lower limit of detection of 73 genomes per reaction at cycle threshold (Ct) value of 35, with 100% average reaction efficiency and an average R2 of 0.9925. 99.7% (624/626) of Nm isolates tested were sodC-positive, with a range of average Ct values from 13.0 to 29.5. The mean sodC Ct value of these Nm isolates was 17.6±2.2 (±SD). Of the 626 Nm tested, 178 were nongroupable (NG) ctrA-negative Nm isolates, and 98.9% (176/178) of these were detected by sodC rt-PCR. The assay was 100% specific, with all 244 non-Nm isolates testing negative. Of 157 clinical specimens tested, sodC detected 25/157 Nm or 4 additional specimens compared to ctrA and 24 more than culture. Among 582 carriage specimens, sodC detected Nm in 1 more than ctrA and in 4 more than culture. This sodC rt-PCR assay is a highly sensitive and specific method for detection of Nm, especially in carriage studies where many meningococcal isolates lack capsule genes

Random Amplified Polymorphic DNA Assay as a Rapid Tool in Screening for Neisseria meningitidis Serogroup C Isolates of Electrophoretic Type 24

Neisseria meningitidis serogroup C (NMSC) isolates of electrophoretic type 24 (ET-24), as identified by multilocus enzyme electrophoresis, are the main cause of serogroup C meningococcal disease outbreaks and sporadic meningococcal disease in the United States. We evaluated a random amplified polymorphic DNA assay as a rapid tool to screen for isolates of ET-24 by testing 199 NMSC isolates of 51 different ETs. A sensitivity of 88% and a specificity of 87% was achieved in identification of ET-24 isolates when the patterns obtained by two primers, P1 and P5, were analyzed together

Meningococcus genome informatics platform:

a system for analyzing multilocus sequence typing dat

Molecular Epidemiology of Neisseria meningitidis Isolates from an Outbreak of Meningococcal Disease among Men Who Have Sex with Men, Chicago, Illinois, 2003▿

We characterized five Neisseria meningitidis serogroup C isolates from a Chicago outbreak of meningococcal disease that occurred in 2003 among a community of men who have sex with men. Isolates from this outbreak were identical to each other but distinct from the clone that caused a similar outbreak in Canada in 2001

Use of Real-Time PCR To Resolve Slide Agglutination Discrepancies in Serogroup Identification of Neisseria meningitidis

Neisseria meningitidis is a leading cause of bacterial meningitis and septicemia in children and young adults in the United States. Rapid and reliable identification of N. meningitidis serogroups is crucial for judicious and expedient response to cases of meningococcal disease, including decisions about vaccination campaigns. From 1997 to 2002, 1,298 N. meningitidis isolates, collected in the United States through the Active Bacterial Core surveillance (ABCs), were tested by slide agglutination serogrouping (SASG) at both the ABCs sites and the Centers for Disease Control and Prevention (CDC). For over 95% of isolates, SASG results were concordant, while discrepant results were reported for 58 isolates. To resolve these discrepancies, we repeated the SASG in a blinded fashion and employed ctrA and six serogroup-specific PCR assays (SGS-PCR) to determine the genetic capsule type. Seventy-eight percent of discrepancies were resolved, since results of the SGS-PCR and SASG blinded study agreed with each other and confirmed the SASG result at either state health laboratories or CDC. This study demonstrated the ability of SGS-PCR to efficiently resolve SASG discrepancies and identified the main cause of the discrepancies as overreporting of these isolates as nongroupable. It also reemphasized the importance of adherence to quality assurance procedures when performing SASG and prompted prospective monitoring for SASG discrepancies involving isolates collected through ABCs in the United States

The Amazon in motion: Changing politics, development strategies, peoples, landscapes, and livelihoods

This chapter reviews the often-invisible, powerful processes that drive social and ecological change in the Amazon, and the diverse peoples who inhabit its landscapes. It explores the large-scale development ideologies of modernization, and the policy tools that were deployed to carry them out. Outlining general periods of macro policy shifts, it shows the evolution of the framework for today’s complex interactions between large-scale agroindustry, mining, and hydrocarbons; diverse small-scale livelihoods; the clandestine and illicit economies of land grabbing, gold, coca and timber; and their operation in globalized and regional economies. While Pan-Amazonian governments have oscillated between authoritarian and more or less democratic forms of governance since the mid-20th century, more democratic transformations and trade have led to interactions among a wide array of new civil society actors; including non-governmental organizations (NGOs), social movements, rural syndicates, and urban social movements; and powerful actors such as national and international technical, financial, and corporate groups and international conservation organizations. New international sources of funding expanded well beyond multilateral or traditional bilateral aid; this includes financing from China and hedge funds, and new forms of both informal and corporate production lending. Integration into numerous globalized markets and finance have had enormous effects on Amazonian politics and economies at all scales. These dynamics have generated new kinds of policies, political framings, institutions, and economies, and restructured old ones; reshaped forms of urbanization, settlements, and land regimes; and stimulated extensive and controversial infrastructure development. On the ground, diverse Amazonian peoples have largely suffered the impacts of these processes, and have continued to adapt to changing circumstances while fighting to advance their own proposals for alternative forms of Amazon conservation and development